The factory fogs are constructed kind of weird and they fit in the cutout openings, they are also not that good for lighting.
Hella, IPF, CIBIE all make much better lights. I run the hella 450's and they fit right in the same spot but are not recessed.
As far as wiring goes, none of it is in place. If you look in the power distribution center, passenger side between the battery and firewall, you will see two blank socket holes for fog light relays, look closer and you will see that there are no relay sockets under there. Jeep has an aftermarket wiring kit that has a new switch panel that replaced your old one and has an extra hole for the fog light switch. It also has a couple of relays and it all pretty much goes inside, it leaves ONE yellow wire that you feed thru the firewall for trigging an external relay. In my case I used the outside part of the hella kit which was a fused relay and their wires to connect the fogs.
The directions are OK but it helps to have a factory manual for deciphering the connection points they refer to. BTW I started out with Hella 550's but the lenses cracked after I left them on while parked one day with the covers installed, melted the covers and cracked the lenses. I bought a set of 450's to replace them.